|
Status |
Public on Sep 17, 2024 |
Title |
NUC1-nuc2_P40_Rep4 |
Sample type |
SRA |
|
|
Source name |
Leaf
|
Organism |
Zea mays |
Characteristics |
tissue: Leaf u. maydis_strain: NUC1-nuc2 fraction: P40 genotype: B73
|
Treatment protocol |
The Z. mays seedlings were infected with a suspension of U. maydis sporidia in sterile water using a syringe infection method.
|
Growth protocol |
Z. mays seedlings were grown under controlled temperature and humidity conditions throughout with a 16 h light and 8 h dark cycle. U. maydis sporidia were grown at 28ºC under constant shaking at 200 rpm till OD600 of the culture reached 0.8. At this stage the cells were harvested and used for infection.
|
Extracted molecule |
total RNA |
Extraction protocol |
RNA was extracted from all the different samples using TRIzol method following the manufacturer’s protocol. We used the commertial kit NEB Ultra II stranded
|
|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
NextSeq 2000 |
|
|
Data processing |
Untrimmed reads were mapped to the Maize Genome v4 using Hisat2 with default parameters. The resulting bam file was analyzed using Strigtie package and the gff3 file from AGP v4 version with default paramenters, resulting in a mapping gtf file for each sample. Assembly: Zea_mays.AGPv4.dna.toplevel.fa Supplementary files format and content: gtf files of mapping reads
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|
|
Submission date |
Sep 13, 2024 |
Last update date |
Sep 17, 2024 |
Contact name |
Patricia Baldrich Gonzalez |
E-mail(s) |
pbaldrich@ucdavis.edu
|
Organization name |
University of California - Davis
|
Department |
Genome Center
|
Lab |
Meyers Lab
|
Street address |
451 Health Sciences Dr., Davis, CA 95616
|
City |
Davis |
State/province |
CA |
ZIP/Postal code |
95616 |
Country |
USA |
|
|
Platform ID |
GPL34900 |
Series (1) |
GSE277127 |
Evaluating the effect of secreted ribonucleases from Ustilago maydis on the extracellular RNA profile/repertoire of Zea mays during corn smut disease |
|
Relations |
BioSample |
SAMN43760909 |
SRA |
SRX26078388 |